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khmer v1.0.1 release notes
==========================

This is bugfix release. Note: the installation instructions have been
slightly simplified.

https://khmer.readthedocs.org/en/v1.0.1/

New items of note:
------------------

This release successfully installs and passes its unit tests on Debian
6.0 "Squeeze", Debian 7.0 "Wheezy", Fedora 19, OS X 7 "Lion", OS X 8
"Mountain Lion", Red Hat Enterprise Linux 6, Scientific Linux 6, Ubuntu
10.04 LTS, and Ubuntu 12.04 LTS. Thanks to the `UW-Madison Build and
Test Lab <https://www.batlab.org/>`__ for their `testing
infrastructure <http://submit-1.batlab.org/nmi/results/details?runID=247153>`__.

Notable bugs fixed/issues closed:
---------------------------------

fixed thread hanging issue #406 @ctb Explicit python2 invocation #404
@mr-c MANIFEST.in,setup.py: fix to correct zlib packaging #365 @mr-c
fixed check\_space\_for\_hashtable to use args.n\_tables #382 @ctb Bug
fix: make-initial-stoptags.py error on missing .ht input file, actual
input file is .pt #391 @mr-c

Minor updates
-------------

include calc-best-assembly.py in v1.0.1 #409 @ctb updated
normalize-by-median documentation for loadtable #378 @ctb updated
diginorm for new FP rate info; corrected spelling error #398 @ctb Add
spellcheck to code review checklist. #397 @ctb

Known Issues
------------

All of these are pre-existing.

Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
https://github.com/dib-lab/khmer/issues/266

Some FASTQ files confuse our parser when running with more than one
thread. For example, while using load-into-counting.py. If you
experience this then add "--threads=1" to your command line. This issue
is being tracked in https://github.com/dib-lab/khmer/issues/249

If your k-mer table (hashfile) gets truncated, perhaps from a full
filesystem, then our tools currently will get stuck. This is being
tracked in https://github.com/dib-lab/khmer/issues/247 and
https://github.com/dib-lab/khmer/issues/246

Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
https://github.com/dib-lab/khmer/issues/23

annotate-partitions.py only outputs FASTA even if given a FASTQ file.
This issue is being tracked in
https://github.com/dib-lab/khmer/issues/46

A user reported that abundance-dist-single.py fails with small files and
many threads. This issue is being tracked in
https://github.com/dib-lab/khmer/issues/75

Contributors
------------

@mr-c, @ctb, @luizirber, @RamRS, @ctSkennerton